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package structures;
import dna.Data;
import fileIO.ReadWrite;
import shared.KillSwitch;
import shared.Tools;
public class CoverageArray2 extends CoverageArray {
/**
*
*/
private static final long serialVersionUID = 8242586595591123194L;
public static void main(String[] args){
runSpeedTest(args);
// translateGenomeBuild(args);
}
public static void runSpeedTest(String[] args){
long time1=System.nanoTime();
CoverageArray2 ca=(CoverageArray2)read(args[1]);
ca.chromosome=Byte.parseByte(args[0]);
long time2=System.nanoTime();
// int dot=args[1].lastIndexOf(".");
// String outfile=args[1].substring(0,dot)+".ca";
args[1]=args[1].replace('\\', '/');
int slash=args[1].lastIndexOf('/');
String outfile;
if(slash<1){
outfile="coverage-chr"+ca.chromosome+"-build"+Data.GENOME_BUILD+".ca";
}else{
outfile=args[1].substring(0,slash+1)+"coverage-chr"+ca.chromosome+"-build"+Data.GENOME_BUILD+".ca";
}
System.out.println("minIndex="+ca.minIndex+", maxIndex="+ca.maxIndex+", length="+ca.array.length+
"; time="+Tools.format("%.3f seconds", (time2-time1)/1000000000d));
long time3=System.nanoTime();
ReadWrite.write(ca, outfile, false);
ca=null;
System.gc();
ca=(CoverageArray2)read(outfile);
long time4=System.nanoTime();
System.out.println("minIndex="+ca.minIndex+", maxIndex="+ca.maxIndex+", length="+ca.array.length+
"; time="+Tools.format("%.3f seconds", (time4-time3)/1000000000d));
}
public CoverageArray2(int chrom, int len){
super(chrom, len);
array=KillSwitch.allocChar1D(len);
}
/**
* @param loc
* @param amt
*/
@Override
public void increment(int loc, int amt) {
set(loc, get(loc)+amt);
}
/**
* @param loc
*/
@Override
public void increment(int loc) {
set(loc, get(loc)+1);
}
@Override
public synchronized void incrementRangeSynchronized(int min, int max, int amt) {
incrementRange(min, max, amt);
}
@Override
public void incrementRange(int min, int max, int amt) {
if(min<0){min=0;}
if(max>=array.length){//Increase size
int newlen=1+(7*max(array.length, max))/4;
assert(newlen>max);
resize(newlen);
assert(array.length==newlen);
}else if(max<0){max=-1;}
for(int i=min; i<=max; i++){
int val=array[i]+amt;
if(val>Character.MAX_VALUE){
val=Character.MAX_VALUE;
if(!OVERFLOWED){
System.err.println("Note: Coverage capped at "+(int)(Character.MAX_VALUE)+"; please use the flag 32bit for higher values.");
OVERFLOWED=true;
}
}
array[i]=(char)val;
}
minIndex=min(min, minIndex);
maxIndex=max(max, maxIndex);
}
@Override
public void set(int loc, int val){
if(loc>=array.length){//Increase size
int newlen=1+(7*max(array.length, loc))/4;
assert(newlen>loc);
resize(newlen);
assert(array.length==newlen);
}else if(loc<0){
// minIndex=min(0, minIndex);
// maxIndex=max(0, maxIndex);
return;
}
if(val>Character.MAX_VALUE && !OVERFLOWED){
System.err.println("Note: Coverage capped at "+(int)(Character.MAX_VALUE)+"; please use the flag 32bit for higher values.");
OVERFLOWED=true;
}
array[loc]=(val>Character.MAX_VALUE ? Character.MAX_VALUE : (char)val);
minIndex=min(loc, minIndex);
maxIndex=max(loc, maxIndex);
}
@Override
public int get(int loc){
return loc>=array.length || loc<0 ? 0 : array[loc];
}
@Override
public void resize(int newlen){
// System.err.println("Resized CoverageArray "+chromosome+" to "+newlen);
char[] temp=KillSwitch.allocChar1D(newlen);
int lim=min(array.length, newlen);
assert(lim>maxIndex) : lim+","+maxIndex;
for(int i=0; i<lim; i++){
temp[i]=array[i];
}
array=temp;
}
@Override
public String toString(){
StringBuilder sb=new StringBuilder();
sb.append('[');
for(int i=0; i<=maxIndex; i++){
if(i>0){sb.append(", ");}
sb.append((int)array[i]);
}
sb.append(']');
return sb.toString();
}
@Override
public char[] toArray() {return array;}
public char[] array;
// @Override
// public int length(){return maxIndex-minIndex+1;}
@Override
public int arrayLength(){return array.length;}
private static boolean OVERFLOWED=false;
/**
*
*/
// private static final long serialVersionUID = -7493066925636540386L;
}
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